Sesame (Sesamum indicum L.) contains abundant lignans including lipid-soluble lignans (sesamin and sesamolin) and water-soluble lignan glycosides (sesaminol triglucoside and sesaminol diglucoside) related to antioxidative activity. In this study, near infrared reflectance spectroscopy (NIRS) was used to develop a rapid and nondestructive method for the determination of lignan contents on intact sesame seeds. Ninety-three intact seeds were scanned in the reflectance mode of a scanning monochromator. This scanning procedure did not require the pulverization of samples, allowing each analysis to be completed within minutes. Reference values for lignan contents were obtained by high-performance liquid chromatography analysis. Calibration equations for lignans (sesamin and sesamolin) and lignan glycosides (sesaminol triglucoside and sesaminol diglucoside) contents were developed using modified partial least squares regression with internal cross-validation (n = 63). The equations obtained had low standard errors of cross-validation and moderate R2 (coefficient of determination in calibration). The prediction of an external validation set (n = 30) showed significant correlation between reference values and NIRS predicted values based on the SEP (standard error of prediction), bias, and r2 (coefficient of determination in prediction). The models developed in this study had relatively higher values (more than 2.0) of SD/SEP(C) for all lignans and lignan glycosides except for sesaminol diglucoside, which had a minor amount, indicating good correlation between the reference and the NIRS estimate. The results showed that NIRS, a nondestructive screening method, could be used to rapidly determine lignan and lignan glycoside contents in the breeding programs for high quality sesame.